Research Topics
| J SkolnickSummaryAffiliation: Donald Danforth Plant Science Center Country: USA Publications
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Detail Information
Publications
From genes to protein structure and function: novel applications of computational approaches in the genomic eraJ Skolnick
Danforth Plant Science Center, Laboratory of Computational Genomics, St Louis, MO 63108, USA
Trends Biotechnol 18:34-9. 2000..Structural descriptors for protein functional sites are crucial for unlocking the secrets in both the sequence and structural-genomics projects...- Derivation of protein-specific pair potentials based on weak sequence fragment similarityJ Skolnick
Laboratory of Computational Genomics, Danforth Plant Science Center, St Louis, Missouri 63108, USA
Proteins 38:3-16. 2000..This suggests that such protein-specific potentials provide a significant advantage relative to generic quasichemical potentials... - Structural genomics and its importance for gene function analysisJ Skolnick
Laboratory of Computational Genomics, The Danforth Plant Science Center, 893 N, Warson Rd, St Louis, MO 63141, USA
Nat Biotechnol 18:283-7. 2000..When applied to genomes, structural information (either experimental or predicted) is likely to play an important role in high-throughput function assignment... - Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinementJ Skolnick
Donald Danforth Plant Science Center, Saint Louis, Missouri 63141, USA
Proteins . 2001..For the most difficult targets from the new fold categories, substantial fragments of structures have been correctly predicted. Possible improvements of the method are briefly discussed... - Generalized comparative modeling (GENECOMP): a combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinementA Kolinski
Laboratory of Computational Genomics, Donald Danforth Plant Science Center, St. Louis, Missouri 63141, USA
Proteins 44:133-49. 2001..The procedure is readily automated and can be implemented on a genomic scale... - TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraintsD Kihara
Laboratory of Computational Genomics, Donald Danforth Plant Science Center, 893 North Warson Road, St. Louis, MO 63141, USA
Proc Natl Acad Sci U S A 98:10125-30. 2001.... - A distance-dependent atomic knowledge-based potential for improved protein structure selectionH Lu
Laboratory of Computational Genomics, Donald Danforth Plant Science Center, St. Louis, Missouri 63141, USA
Proteins 44:223-32. 2001..As such, it can be used to select near-native folds generated by structure prediction algorithms as well as for protein structure refinement... - Defrosting the frozen approximation: PROSPECTOR--a new approach to threadingJ Skolnick
Laboratory of Computational Genomics, Danforth Plant Science Center, Creve Coeur, Missouri 63141, USA
Proteins 42:319-31. 2001..Finally, a web server has been established for use by the academic community (http://bioinformatics.danforthcenter.org/services/threading.html)... - BioMolQuest: integrated database-based retrieval of protein structural and functional informationY V Bukhman
Laboratory of Computational Genomics, Donald Danforth Plant Science Center, 893 N. Warson Rd, St Louis, MO 63141, USA
Bioinformatics 17:468-78. 2001..The search engine achieves significant improvements in query performance by automatically utilizing cross-references between the legacy databases. The results of the queries are presented in an organized, hierarchical way... - Ab initio protein structure prediction using chunk-TASSERHongyi Zhou
Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
Biophys J 93:1510-8. 2007..Chunk-TASSER is approximately 11% (10%) better than TASSER for the total TM-score of the first (best of top five) models. Chunk-TASSER is fully automated and can be used in proteome scale protein structure prediction... - Unfolding of globular proteins: monte carlo dynamics of a realistic reduced modelAndrzej Kolinski
Laboratory of Theory of Biopolymers, Faculty of Chemistry, Warsaw University, Warsaw, Poland
Biophys J 85:3271-8. 2003..The correlation with various experiments, especially for sequence-specific effects, strongly suggests that properly designed reduced models of proteins can be used for qualitative studies (or prediction) of protein unfolding pathways... - A simple lattice model that exhibits a protein-like cooperative all-or-none folding transitionAndrzej Kolinski
Faculty of Chemistry, Warsaw University, Pasteura 1, 02 093 Warsaw, Poland
Biopolymers 69:399-405. 2003.... - Multimeric threading-based prediction of protein-protein interactions on a genomic scale: application to the Saccharomyces cerevisiae proteomeLong Lu
Center of Excellence in Bioinformatics, University at Buffalo, Buffalo, New York 14203, USA
Genome Res 13:1146-54. 2003..Finally, several relevant predictions involved in various functions are presented. In summary, we provide a novel approach to predict protein-protein interactions on a genomic scale that is a useful complement to experimental methods... - A minimal physically realistic protein-like lattice model: designing an energy landscape that ensures all-or-none folding to a unique native statePiotr Pokarowski
Institute of Applied Mathematics and Mechanics, Warsaw University, Banacha 2, Poland
Biophys J 84:1518-26. 2003..Simulations were performed via the Replica Exchange Monte Carlo method and the numerical data analyzed via a multihistogram method... - Computer simulations of protein folding with a small number of distance restraintsAndrzej Sikorski
Department of Chemistry, Warsaw University, L Pasteura 1, 02 093 Warszawa, Poland
Acta Biochim Pol 49:683-92. 2002..A small improvement (about 0.5 A) was also achieved in the RMSD of the folds. The proposed method can be used for the refinement of structures determined experimentally from NMR data... - Ab initio protein structure prediction on a genomic scale: application to the Mycoplasma genitalium genomeDaisuke Kihara
Laboratory of Computational Genomics, Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, USA
Proc Natl Acad Sci U S A 99:5993-8. 2002..8% of the 29 proteins) may have correct folds. Thus, the topology of a total of 58 proteins probably has been correctly predicted. Based on these results, ab initio protein structure prediction is becoming a practical approach... - Numerical study of the entropy loss of dimerization and the folding thermodynamics of the GCN4 leucine zipperJorge Viñals
Laboratory of Computational Genomics, Donald Danforth Plant Science Center, St Louis, MO 63132, USA
Biophys J 83:2801-11. 2002.... - Can a physics-based, all-atom potential find a protein's native structure among misfolded structures? I. Large scale AMBER benchmarkingLiliana Wroblewska
Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30318, USA
J Comput Chem 28:2059-66. 2007..Ways of correcting the potential function in order to make it more suitable for protein model refinement are proposed... - Origin of intrinsic 3(10)-helix versus strand stability in homopolypeptides and its implications for the accuracy of the Amber force fieldAnna Jagielska
Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250 14th Street, Atlanta, Georgia 30318, USA
J Comput Chem 28:1648-57. 2007..Therefore, extant molecular mechanics force fields, such as Amber, need refinement of their parameters to correctly describe helix-extended state energetics and geometry of major conformations... - Phosphoprotein and phosphopeptide interactions with the FHA domain from Arabidopsis kinase-associated protein phosphataseZhaofeng Ding
Department of Biochemistry, Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
Biochemistry 46:2684-96. 2007..15N-Labeled KI-FHA was titrated with the GST-BRI1 kinase domain and monitored by NMR. BRI1 interacts with the same 3/4, 4/5, 6/7, 8/9, and 10/11 recognition loops of KI-FHA, with similar affinity as the phosphoThr peptides... - All-atom ab initio folding of a diverse set of proteinsJae Shick Yang
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
Structure 15:53-63. 2007..Our results demonstrate that the successful folding of a protein chain to its native state is governed by only a few crucial energetic terms... - TASSER-Lite: an automated tool for protein comparative modelingShashi Bhushan Pandit
Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, GA 30318, USA
Biophys J 91:4180-90. 2006..TASSER-Lite is provided on the web at (http://cssb.biology.gatech.edu/skolnick/webservice/tasserlite/index.html)... - In quest of an empirical potential for protein structure predictionJeffrey Skolnick
Center of Excellence in Bioinformatics, University at Buffalo, 901 Washington Street, Buffalo, NY 14203, USA
Curr Opin Struct Biol 16:166-71. 2006..This represents significant progress and suggests applications to proteome-scale structure prediction... - Benchmarking of TASSER in the ab initio limitJose M Borreguero
Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30318, USA
Proteins 68:48-56. 2007..Thus, it is the effective configurational entropy of the protein that dictates the average likelihood of correctly arranging the secondary structure elements... - Ab initio modeling of small proteins by iterative TASSER simulationsSitao Wu
Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, Lawrence, KS 66047, USA
BMC Biol 5:17. 2007..The aim of this study was to extend the TASSER (threading/assembly/refinement) method for the ab initio modeling and examine systemically its ability to fold small single-domain proteins... - Analysis of TASSER-based CASP7 protein structure prediction resultsHongyi Zhou
Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30318, USA
Proteins 69:90-7. 2007..For the more difficult targets, TASSER with modest human intervention performed better in comparison to its server counterpart, MetaTASSER, which used a limited time simulation... - Protein model quality assessment prediction by combining fragment comparisons and a consensus C(alpha) contact potentialHongyi Zhou
Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30318, USA
Proteins 71:1211-8. 2008..83 for the 98 targets, which is better than those of other quality assessment methods that participated in CASP7. Our method also outperforms the other methods by about 3% as assessed by the total GDT-score of the selected top models... - DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactionsMu Gao
Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250 14th Street NW, Atlanta, GA 30318, USA
Nucleic Acids Res 36:3978-92. 2008..DBD-Hunter is freely available at http://cssb.biology.gatech.edu/skolnick/webservice/DBD-Hunter/... - A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotationMichal Brylinski
Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250 14th Street NW, Atlanta, GA 30318, USA
Proc Natl Acad Sci U S A 105:129-34. 2008..Furthermore, the chemical properties of template-bound ligands can be used to select ligand templates associated with the binding site. In most cases, FINDSITE can accurately assign a molecular function to the protein model... - Assessment of programs for ligand binding affinity predictionRyangGuk Kim
Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250 14th Street, Atlanta, Georgia 30318, USA
J Comput Chem 29:1316-31. 2008.... - Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraintsMichal Brylinski
Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250 14th Street NW, Atlanta, Georgia 30318, USA
J Comput Chem 29:1574-88. 2008..The success rate of Q-Dock employing a pocket-specific potential is 6.3 times higher than that previously reported for the Dolores method, another low-resolution docking approach... - Fast procedure for reconstruction of full-atom protein models from reduced representationsPiotr Rotkiewicz
Burnham Institute for Medical Research, 10901 N Torrey Pines Road, La Jolla, California 92037, USA
J Comput Chem 29:1460-5. 2008..The method is implemented as a standalone program that is available for download from http://cssb.biology.gatech.edu/skolnick/files/PULCHRA... - On the origin and highly likely completeness of single-domain protein structuresYang Zhang
Center of Excellence in Bioinformatics, University at Buffalo, State University of New York, 901 Washington Street, Buffalo, NY 14203, USA
Proc Natl Acad Sci U S A 103:2605-10. 2006..Thus, the presence of active-site-like geometries also seems to be a consequence of the packing of compact, secondary structural elements. These results have significant implications for the evolution of protein structure and function... - Benchmarking of dimeric threading and structure refinementVera Grimm
Center of Excellence in Bioinformatics, University at Buffalo, Buffalo, New York, USA
Proteins 63:457-65. 2006..Preliminary results for three full-length dimeric models generated with the TASSER method show on average a significant improvement of the final model over the initial template... - MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threadingLong Lu
Laboratory of Computational Genomics, Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
Proteins 49:350-64. 2002..An estimation of the false-negative rate for yeast-predicted interactions has also been provided. Thus, a promising approach to help assist in the assignment of protein-protein interactions on a genomic scale has been developed... - Development of unified statistical potentials describing protein-protein interactionsHui Lu
Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
Biophys J 84:1895-901. 2003..However, the more time-consuming atom-based potential performs better in identifying near-native structures from docking generated decoys... - TOUCHSTONE II: a new approach to ab initio protein structure predictionYang Zhang
Center of Excellence in Bioinformatics, University at Buffalo, Buffalo, New York 14203, USA
Biophys J 85:1145-64. 2003..These procedures are readily automated and are being implemented on a genomic scale... - TOUCHSTONEX: protein structure prediction with sparse NMR dataWei Li
Center of Excellence in Bioinformatics, University at Buffalo, Buffalo, New York 14203, USA
Proteins 53:290-306. 2003.... - The PDB is a covering set of small protein structuresDaisuke Kihara
Center of Excellence in Bioinformatics, University at Buffalo, 901 Washington St, Suite 300, Buffalo, NY 14203, USA
J Mol Biol 334:793-802. 2003..5A for proteins up to 320 residues long. These results give a new view of the nature of protein structure space, and its implications for protein structure prediction are discussed... - Use of residual dipolar couplings as restraints in ab initio protein structure predictionTurkan Haliloglu
Polymer Research Center and Chemical Engineering Department, Bogazici University, Bebek 80815, Istanbul, Turkey
Biopolymers 70:548-62. 2003..The latter, in particular, has possible implications for the structure-based functional analysis of predicted structures... - SPICKER: a clustering approach to identify near-native protein foldsYang Zhang
Center of Excellence in Bioinformatics, University at Buffalo, 901 Washington St, Buffalo, New York 14203, USA
J Comput Chem 25:865-71. 2004..Although native fold identification from divergent decoy structures remains a challenge, our overall results show significant improvement over our previous clustering algorithms... - Microbial genomes have over 72% structure assignment by the threading algorithm PROSPECTOR_QDaisuke Kihara
UB Center of Excellence in Bioinformatics, University at Buffalo, Buffalo, New York 14215, USA
Proteins 55:464-73. 2004..The fold distribution of the genomes and the effect of the number of homologous sequences on structure assignment are also discussed... - Automated structure prediction of weakly homologous proteins on a genomic scaleYang Zhang
Center of Excellence in Bioinformatics, University at Buffalo, 901 Washington Street, Buffalo, NY 14203, USA
Proc Natl Acad Sci U S A 101:7594-9. 2004.... - Local propensities and statistical potentials of backbone dihedral angles in proteinsMarcos R Betancourt
University at Buffalo Center of Excellence in Bioinformatics, 901 Washington St, Suite 300, Buffalo, NY 14203, USA
J Mol Biol 342:635-49. 2004..In general, most alpha-helices and many beta-sheets are strongly determined by the local potential, while the conformations in loops and near the end of beta-sheets are more influenced by non-local interactions... - Tertiary structure predictions on a comprehensive benchmark of medium to large size proteinsYang Zhang
Center of Excellence in Bioinformatics, University at Buffalo, Buffalo, New York 14203, USA
Biophys J 87:2647-55. 2004.... - Scoring function for automated assessment of protein structure template qualityYang Zhang
Center of Excellence in Bioinformatics, University at Buffalo, Buffalo, New York 14203, USA
Proteins 57:702-10. 2004..These data suggest that the TM-score is a useful complement to the fully automated assessment of protein structure predictions. The executable program of TM-score is freely downloadable at http://bioinformatics.buffalo.edu/TM-score... - The protein structure prediction problem could be solved using the current PDB libraryYang Zhang
Center of Excellence in Bioinformatics, University at Buffalo, 901 Washington Street, Buffalo, NY 14203, USA
Proc Natl Acad Sci U S A 102:1029-34. 2005..These results are highly suggestive that the protein-folding problem can in principle be solved based on the current PDB library by developing efficient fold recognition algorithms that can recover such initial alignments... - Putting the pathway back into protein foldingJeffrey Skolnick
Center of Excellence in Bioinformatics, University at Buffalo, 901 Washington Street, Buffalo, NY 14203, USA
Proc Natl Acad Sci U S A 102:2265-6. 2005 - TM-align: a protein structure alignment algorithm based on the TM-scoreYang Zhang
Center of Excellence in Bioinformatics, University at Buffalo 901 Washington Street, Buffalo, NY 14203, USA
Nucleic Acids Res 33:2302-9. 2005..This correlation could be used to assist in model selection in blind protein structure predictions. The TM-align program is freely downloadable at http://bioinformatics.buffalo.edu/TM-align... - TASSER: an automated method for the prediction of protein tertiary structures in CASP6Yang Zhang
Center of Excellence in Bioinformatics, University at Buffalo, Buffalo, New York 14203, USA
Proteins 61:91-8. 2005..47 [fold recognition (FR), 37 targets/domains], and 0.30 [new fold (NF), 10 targets/domains]. This highlights the need to develop novel (or improved) approaches to identify very distant targets as well as better NF algorithms... - Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein foldingYang Zhang
Laboratory of Computational Genomics, Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
Proteins 48:192-201. 2002..This mrRMSD correlation may be useful in blind prediction as an indicator of the likelihood of successful folds...